Mr Estrada has been impeached by the House of Representatives, accused of accepting millions of dollars in bribes from illegal gambling syndicates.
Mr Estrada has been impeached by the House of Representatives, accused of accepting millions of dollars in bribes from illegal gambling syndicates.
The country's Vice-President, Gloria Macapagal Arroyo, says he must resign for the sake of stability and the economy.
Reports said about 15,000 protesters gathered near the presidential palace in Manila, where they burned effigies of Mr Estrada.
Traders at the stock exchange walked out, clapping their hands and chanting "Erap resign" - Erap is Mr Estrada's nickname from his days as a movie star.
Many wore black arm bands in mourning for the economy which has been plunged into turmoil by the scandal.
Strike
Major protests were also held in Manila's financial district and the central cities of Bacolod and Iloilo.
Many offices and shops closed to allow employees to join the rallies.
The nationwide strikes disrupted transport in several cities and many schools were shut.
Up to 70% of public transport was at a standstill in the southern cities of General Santos and Cotabato.
But banks and airports were said to be functioning normally and loading at ports was only minimally affected.
Troops and police were on alert to avert clashes, but there were no reports of trouble.
Impeachment
Earlier, President Estrada appealed to labour unions not to go through with the strike.
The general strike came a day after Mr Estrada was impeached by the House of Representatives over allegations of corruption.
The president has been accused of taking more than $8m in bribes from operators of an illegal lottery game which is played across the country.
He has repeatedly said he is innocent and is confident his name will be cleared.
Senate President Aquilino Pimentel told Reuters the impeachment trial was likely to begin on 1 December.
He said the Senate would probably deliver a verdict by the first week of February.
Mr Estrada is the fourth president in the country's turbulent political history to have been threatened with impeachment.
But the proceedings against the other three, including Ferdinand Marcos, were thrown out before they got to the senate stage.